330 Hours: Don dies an extremely horrifying and gruesome death, and even Jack is horrified by it. It helps that it wasn't even his fault that he was a villain in the first place, and he was essentially being controlled by the government.
At the end of The Suffering Game, Lydia dies of despair when Edward is killed; in her final moments, she drops her illusory form in favor of her true black robes, and, at a loss for words, simply screams.
John might be the source and avatar of the Hunger, but watching him get subsumed by it is more than a little tragic. His actual death, watching the sunset with Merle before fading away, only makes him more sympathetic.
Although a lot of the villains in Arby 'n' the Chief are usually downright over-the-top like Craig, or downright hateful like Adam, the series's final villain, Eugene Black is certainly an interesting case of this. As evident throughout the show's final season, he's a downright sadist who has no trouble letting his psychopathic or pedophile friends do as they wish to people online, as well as enjoys forcing hundreds of innocent people to replace their Xbox 360s after banning them with a hardware corrupting software over a period of 2 months, just for laughs. On the flipside though, he's also a failing student at his school (despite also being a bully too), is constantly abused by his Drunk (and sometimes neglectful) Father, and his sister (the only source of happiness in his life) is dying a slow and agonizing death of Leukemia. It's hard whether to feel sorry for him for how crappy his life is, or to hate him for how much of a bastard he is just to repress these feelings. To add insult to injury, this only get worse for him, and he's Driven to Suicide by the show's end.
Ask That Guy with the Glasses goes out with a strange mix of this and Death as Comedy. In the Grand Finale, someone asks him "do you have a question?". He gets so excited that someone finally thought about what he wanted that he literally explodes. Lampshaded by Chester A. Bum, who is sad when he first finds out about That Guy's death, but then realizes that he was a terrible person and it's probably a good thing he's gone.
Critical Role has one with Delilah Briarwood. She and her husband Sylas are, by all accounts, a loving couple who care for one another very, very deeply. They are also truly terrible people, and are the ones responsible for the massacre of protagonist Percy's family and household and the trauma he endured as a result, as well as unknown other evils. But even after the horrible things they did, critters and players felt bad for Delilah, due to her absolutely heartbroken reaction when she saw Sylas killed right before her eyes.
The match between Guts and Dimitri sees Dimitri sympathizing with Guts after he Died Standing Up and taking up arms against the demons trying to lay claim to his soul.
Marble Hornets: The two main antagonists of the series, Alex and Brian, both die with some degree of sympathy. Alex practically begs Tim to finish what he started, implying that while he may have gone Ax-Crazy, he nonetheless believed that what he was doing was right. Brian, on the other hand, is revealed to be the Hooded Man shortly after his own demise. Seeing the sharp contrast between his personalities before and after encountering the Operator makes the viewer sympathize with him as well.
In the Season 10 finale of Red vs. Blue, the defeat of the Director emphasises the tragedy that consumed his life. Carolina finds him locked in a bunker watching on endless repeat the video of the last time he ever saw his wife alive. He realises he has been futilely chasing a ghost for years and neglected his relationship with his daughter. He asks Carolina for a pistol, makes peace with her and and F.I.L.L.S, and then is heavily implied to commit suicide.
Adam Taurus is a Fantastic Terrorist who wants to enslave humanity to the Faunus. However, he becomes increasingly obsessed with destroying Blake for leaving him, permanently maiming her team-mate Yang and trying to assassinate her parents. The final confrontation between him, Blake and Yang stops being a Catharsis Factor when he reveals that his mask was hiding a Schnee Dust Company brand across his left eye. Although it doesn't excuse his abuse and terrorism, it does reveal that humans had subjected him to terrible abuse, setting him on the road to becoming a monster. The creators confirmed they did want the audience to feel some pathos for him at the end.
Ironwood descends into villainy in his single-minded drive to save Atlas, the Relics and the Winter Maiden from Salem; it leaves him broken, isolated and utterly abandoned. He fails to save either Atlas or the Relics, and he is abandoned by the heroes, Winter Maiden, and even Winter, who manage to save thousands of lives without him. Injured and defeated, he watches from the ground as Salem collects the Relics from Cinder and departs without ever acknowledging his existence; even the normally boastful Cinder simply declares "And that's checkmate." before leaving him to his fate on a crashing Atlas.
One of the two major antagonists of Volume 9 gets a degree of pathos at the end. After the Curious Cat is beaten down, their last exchange with Ruby highlights their ruined mental state, heavily implying they know on some level that they're as broken as they claim humans are but they can't do anything about it. Moments later, the Cat is devoured by Neo's Jabberwalker clones while screaming in terror, a swift but brutal affair which Team RWBY react to with horror. Post-mortem, the Blacksmith expresses sorrow for the Cat's turn for the worse and the fact they couldn't be fixed by the Tree, and the flashback of the Cat's beginnings which highlights their original character hammers home the tragedy of their "unfortunate change" due to circumstances that were beyond their ability to change.
Laeil Burbank goes out with a fairly tragic death, accented by how violently and sadistically she received her fatal injury and how she was almost saved. Found here.
Clio Gabriella gets a fairly touching send-off, dying in her boyfriend's arms while she begs for him to save her after being shot. Again, readable here.
Scion of Worm was unquestionably a sadistic, Omnicidal Maniac, but the way that Taylor defeated him by taunting him with the death of his counterpart makes it hard not to pity him.
